[gmx-users] Gromacs configuration error....configure error : cannot compute sizeof ( off_t)...

[rama david]

Hi Gromacs Friends,

After your reply, Itried in another way .
I install the openmpi and fftw3  to the /opt/..

at the time of make  (for gromacs) I encouner with error suggesting to
recompile with -fPIC..

As per instruction in website, I added glag --enable-shared to the
fftw, but again at the time of
gromacs configuration I encounter the sane error   suggesting to
recompile with -fPIC


So I used following coomand line ( as per instruction in website)

./configure --with-fft=fftw3 --enable-mpi --program-suffix=_mpi
--prefix=/opt/gmx_4.5.4 --disable-shared

make
make install
make tests
make links

make install-mdrun
make links
output .....


Libraries have been installed in:
   /opt/gmx_4.5.4/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the `LD_RUN_PATH' environment variable
     during linking
   - use the `-Wl,--rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to `/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
test -z "/opt/gmx_4.5.4/lib/pkgconfig" || /usr/bin/mkdir -p
"/opt/gmx_4.5.4/lib/pkgconfig"
 /usr/bin/install -c -m 644 libgmx_mpi.pc '/opt/gmx_4.5.4/lib/pkgconfig'
make[3]: Leaving directory `/opt/gromacs-4.5.4/src/gmxlib'
make[2]: Leaving directory `/opt/gromacs-4.5.4/src/gmxlib'
make[1]: Leaving directory `/opt/gromacs-4.5.4/src/gmxlib'
(cd ./src/mdlib && make install ; exit 0)
make[1]: Entering directory `/opt/gromacs-4.5.4/src/mdlib'
make[2]: Entering directory `/opt/gromacs-4.5.4/src/mdlib'
test -z "/opt/gmx_4.5.4/lib" || /usr/bin/mkdir -p "/opt/gmx_4.5.4/lib"
 /bin/sh ../../libtool   --mode=install /usr/bin/install -c
libmd_mpi.la '/opt/gmx_4.5.4/lib'
/usr/bin/install -c .libs/libmd_mpi.lai /opt/gmx_4.5.4/lib/libmd_mpi.la
/usr/bin/install -c .libs/libmd_mpi.a /opt/gmx_4.5.4/lib/libmd_mpi.a
chmod 644 /opt/gmx_4.5.4/lib/libmd_mpi.a
ranlib /opt/gmx_4.5.4/lib/libmd_mpi.a
PATH="$PATH:/sbin" ldconfig -n /opt/gmx_4.5.4/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /opt/gmx_4.5.4/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the `LD_RUN_PATH' environment variable
     during linking
   - use the `-Wl,--rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to `/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
test -z "/opt/gmx_4.5.4/lib/pkgconfig" || /usr/bin/mkdir -p
"/opt/gmx_4.5.4/lib/pkgconfig"
 /usr/bin/install -c -m 644 libmd_mpi.pc '/opt/gmx_4.5.4/lib/pkgconfig'
make[2]: Leaving directory `/opt/gromacs-4.5.4/src/mdlib'
make[1]: Leaving directory `/opt/gromacs-4.5.4/src/mdlib'
(cd ./src/kernel && make install-libLTLIBRARIES ; exit 0)
make[1]: Entering directory `/opt/gromacs-4.5.4/src/kernel'
test -z "/opt/gmx_4.5.4/lib" || /usr/bin/mkdir -p "/opt/gmx_4.5.4/lib"
 /bin/sh ../../libtool   --mode=install /usr/bin/install -c
libgmxpreprocess_mpi.la '/opt/gmx_4.5.4/lib'
/usr/bin/install -c .libs/libgmxpreprocess_mpi.lai
/opt/gmx_4.5.4/lib/libgmxpreprocess_mpi.la
/usr/bin/install -c .libs/libgmxpreprocess_mpi.a
/opt/gmx_4.5.4/lib/libgmxpreprocess_mpi.a
chmod 644 /opt/gmx_4.5.4/lib/libgmxpreprocess_mpi.a
ranlib /opt/gmx_4.5.4/lib/libgmxpreprocess_mpi.a
PATH="$PATH:/sbin" ldconfig -n /opt/gmx_4.5.4/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /opt/gmx_4.5.4/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the `LD_RUN_PATH' environment variable
     during linking
   - use the `-Wl,--rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to `/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
make[1]: Leaving directory `/opt/gromacs-4.5.4/src/kernel'
(cd ./src/kernel && make install-mdrun ; exit 0)
make[1]: Entering directory `/opt/gromacs-4.5.4/src/kernel'
/bin/sh ../../config/mkinstalldirs /opt/gmx_4.5.4/bin
if test -f mdrun; then \
  f=`echo mdrun|sed 's/$//;s&$&_mpi&;s/$//'`; \
  echo "  /bin/sh ../../libtool  --mode=install /usr/bin/install -c
mdrun /opt/gmx_4.5.4/bin/$f"; \
   /bin/sh ../../libtool  --mode=install /usr/bin/install -c mdrun
/opt/gmx_4.5.4/bin/$f; \
else :; fi
  /bin/sh ../../libtool  --mode=install /usr/bin/install -c mdrun
/opt/gmx_4.5.4/bin/mdrun_mpi
/usr/bin/install -c mdrun /opt/gmx_4.5.4/bin/mdrun_mpi
make[1]: Leaving directory `/opt/gromacs-4.5.4/src/kernel'
[root at prashant gromacs-4.5.4]# make links
cd /opt/gmx_4.5.4/bin && programs=`ls` && cd /usr/local/bin && \
for i in $programs; do \
   (test ! -f $i && ln -s /opt/gmx_4.5.4/bin/$i . ; exit 0); \
done


When I am giving the command
pdb2gmx_mpi
pdb2gmx_mpi: error while loading shared libraries: libmpi.so.1: cannot
open shared object file: No such file or directory


I have a small experience in linux only, That why I may be missing or
done something wrong???
So please tell me where is the problem ????

Thank you in advane..

With Best wishes and regards,
Rama david.